XB-FEAT-1001094

loc100496109

This is the community wiki page for the gene loc100496109 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase

nomeclature changes

17MAY2023

Xenopus gene name changed from provisional ortholog of cytochrome P450 family 27 subfamily A member 1 to cytochrome P450 family 27 subfamily A member 1 gene 4

Xenopus gene symbol changed from to XB1001094 to cyp27a1.4

See analsyis of synteny and orthology on this wiki page that supports this name change.

synteny and orthology

There are 4 genes/loci tandemly duplicated and provisonally annotated as cyp27a1 in X. tropicalis v10 assembly:

• LOC594905(cyp27a1.3): Entrez Gene: 594905 XP_031749391.1 >>

• XB1001094 [provisional:cyp27a1]: Entrez Gene 100496109, XB-GENEPAGE-1001094; XP_002933985.3

• LOC116407844(cyp27a1): Entrez Gene: 116407844 XP_031749759.1

• XB984297 [provisional:cyp27a1]: Entrez Gene: 100145331 XB-GENEPAGE-984297, XB-GENE-984298 AAI60539.1

In Xlaevis.L there are 3x cyp27a1 genes:

• XB984297.L [provisional:cyp27a1] Entrez Gene:446987 XB-GENEPAGE-984297 XP_041432757.1

• LOC121398019 , Gene ID: 121398019 (no Xb gene page) XP_041432320.1

• cyp27a1 Entrez Gene: 100381137 (no Xb gene page) XP_041433231.1

in Xlaevis.S there is only one cyp27a1 candidate

• LOC108702937 Gene ID: 108702937 XP_041434454.1

Note: LOC121398283(unch)Gene ID: 121398283 XP_041433230.1 (matches 42 Ensembl seqs from Xenopus tropicalis but none have actual names- just ID numbers- so pretty sure this is NOT a CYP gene)

We used synteny and protein sequence alignment to pre-computed homology groups ( using DIOPT EggNog Tool online) to infer orthology and inform naming of these genes.

DIOPT/EggNog matches the each protein for the Xtrop genes (seqs given below) to 3 groups of CYP genes with v. high confidence:

1) ~890 seqs from ~200 species, including Mouse, Pteropus vampyrus (bat), Otolemur garnettii (lemur) and Cavia porcellus (guinea pig) seqs for Cyp27b1, Cyp24a1 and Cyp27a1 (ie including cyp27a1 as suggested by the provisional name for XB1001094 and XB984297)

2) Mouse genes called Cyp27b1, Cyp11b2, Cyp11b1, Cyp24a1, Cyp11a1, Cyp27a1

and

3) >1700 sequences in >800 species, and the majority of genes/proteins (where named) are called CYP11A1, not cyp27a1

To name each gene using Xenopus nomenclature conventions, we looked at synteny patterns:

Mouse CHR1: Stk36> Ttll4> Cyp27a1> Prkag3> > Wnt6> Wnt10a>

Human: TTLL4> CYP27A1> PRKAG3> RPL23AP31> WNT6> WNT10A>

Xtr.chr9: slc22a3< prkag3< ttll4< cnppd1< abcb6< (NB: no sign of the CYP genes near ttll4) [Chr9:83051487..83122986] ////

Xtr.chr9: plcd4> znf142< bcs1l> LOC594905(cyp27a1.3)>< grsf1> XB1001094[cyp27a1.4]< LOC116407845[Grsf1-like(grsf1.2)]> LOC116407844(cyp27a1.2)> XB984297[cyp27a1.1]< wnt6> wnt10a>

In X. laevis the gene read in reverse are in this pattern:

Xla.Chr9_10L: wnt10a.L< wnt6.L< XB984297.L[cyp27a1.1.L]> LOC121398019[cyp27a1.2.L]> grsf1.L> cyp27a1.3.L> LOC121398283(unch)> bcs1l.L< znf142.L<

Xla.Chr9_10S: wnt10a.S< wnt6.S< grsf1.S< LOC108702937(cyp27a1.3.S)> plcd4.S< LOC108702939(ccr4not)

These analyses support naming these genes in Xenopus as cyp27a1, genes 1-4 as indicated above.

The suffixed serial number is designed to keep genes aligned compared to Human and mouse, so the primary ortholog cyp27a1 gene 1 lies immediately adjacent to wnt6, while the cyp27a1.3 gene is between grsf1 and plcd4.

proteins

The proteins associated with thees Xtrop genes are called 'sterol 26-hydroxylase, mitochondrial'

NCBI Reference Sequences

>XP_002933985.3 sterol 26-hydroxylase, mitochondrial [Xenopus tropicalis] MTGLSSLMHSPRLIRNIQAQLTGTMPSASKLGFLPLGRCRWLLHTGRGVSVSQGRAVAGAAVGAVGEEKK MKTFEDLPGPSLLTNIYWVFLRGYILYTHELQAIYKKNYGPMWKSTLGRYKTVNIADVDILETVLRQEGK YPMRSDMEVWKEHRRQRDLSLGPFTEEGHKWHTLRSVLNKRMLKPAEAMLYTGVVNEVVTDFLVRLEEMR SETPSGDMVNDIPNALYRFAFEGISYILFETRIGCLEKQIPVETQRFIDSIGAMLKNSIFVTIFPPWTNN LLPYYKRYMDSWDNIFAFGNKLINEKMKKIEARLERDEEVQGEYLTYLISSGKLTDKEIYGSVAELLLAG VDTTSNTLSWALYHLAREPEIQNALYQEVIGVVPGQNIPTSEDMSSMPLLRAVIKETLRLYPVVPTNSRV AVEKAITIGDYYFPKDTLIALHHYHISRDEKNFPESDKFIPQRWFRESRVKNNPFSSIPFGYGVRACVGR RIAELEMHMCLSRIIKKYEVRPDPSGAEIKSMARIVLTPHKPINLRFLPRTPSPSA

>XP_002933985.3 sterol 26-hydroxylase, mitochondrial [Xenopus tropicalis]

MTGLSSLMHSPRLIRNIQAQLTGTMPSASKLGFLPLGRCRWLLHTGRGVSVSQGRAVAGAAVGAVGEEKK MKTFEDLPGPSLLTNIYWVFLRGYILYTHELQAIYKKNYGPMWKSTLGRYKTVNIADVDILETVLRQEGK YPMRSDMEVWKEHRRQRDLSLGPFTEEGHKWHTLRSVLNKRMLKPAEAMLYTGVVNEVVTDFLVRLEEMR SETPSGDMVNDIPNALYRFAFEGISYILFETRIGCLEKQIPVETQRFIDSIGAMLKNSIFVTIFPPWTNN LLPYYKRYMDSWDNIFAFGNKLINEKMKKIEARLERDEEVQGEYLTYLISSGKLTDKEIYGSVAELLLAG VDTTSNTLSWALYHLAREPEIQNALYQEVIGVVPGQNIPTSEDMSSMPLLRAVIKETLRLYPVVPTNSRV AVEKAITIGDYYFPKDTLIALHHYHISRDEKNFPESDKFIPQRWFRESRVKNNPFSSIPFGYGVRACVGR RIAELEMHMCLSRIIKKYEVRPDPSGAEIKSMARIVLTPHKPINLRFLPRTPSPSA

>XP_031749759.1 sterol 26-hydroxylase, mitochondrial-like isoform X1 [Xenopus tropicalis] MTGLSSLMHSPRLIRNIQAQLTGTMPSASKLGFLPLGRCRWLLHTGRGVSVSQGRAVAGAAVGAVGEEKK MKTFEDLPGPSLLTNIYWVFLRGYILYTHELQAIYKKNYGPMWKSTLGRYKTVNIADVDILETVLRQEGK YPVRIDMEVWKEHRRQRDLSLGPFTEEGHKWHTLRSVLNKRMLKPAEAMLYTGVVNEVVTDFLVRLEEMR SETPSGDMVNDIPNALYRFAFEGISYILFETRIGCLEKQIPVETQRFIDSIGAMLKNYIFVTILPPWTNN LLPYYKRYMDSWDNIFAFGNKLINEKMKKIEARLERDEEVQGEYLTYLISSGKLTDKEIYGSVAELLLAG VDTTSNTLSWALYHLAREPEIQNALYQEVIGVVPGQNIPTSEDISSMPLLRAVIKETLRLYPVVPTNSRV AVEKAITIGDYYFPKDTLIALHHYHISRDEKNFPESDKFIPQRWFRESRVKNNPFSSIPFGYGVRACVGR RIAELEMHMCLSRIIKKYEVRPDPSGAEIKSMARIVLTPHKPINLQFLPRTPSPSA

>AAI60539.1 LOC100145331 protein, partial [Xenopus tropicalis] AVRQTRAAAGGPSRLGCLPQGRGCGLVQAGRGASVSQGRAVTGAAVGATEGRKEMKEFEDLPGPSLLKNL YYYFLRGYLLHTHELQLIYKKMYGPLWRSEIGKYKMVNIADPEVLQRLVRQEGKYPMRNKEDVWKAHRDK RKLAYGPFTEEGHQWYQIRSALNKKMLKPSEAASYAGGINEVVTDFMDRLQDMRKASPSGDMVNDLANAL YRFAFEGISNIVFETRIGCLDKQIPPETQKFIDSIGYMFKNSVYVTFLPHWTRGILPYWDRYIEGWDNIF DFGKHLIDKKMSEIQSRLDKGEEVEGEYLTYLLSSANLTMGEVYGSVCELLLAGVDTTSNTLCWAMYHLA RDPELQQAVYEEVSSAAPMDRIPVAEDIPNMPLLRGVIKETLRLYPVIPTNARIVSEKEVEIGEYRFPKN TLFVLSHYAIARDEENFEDPLKFKPQRWLRDGGMKHHPFSSIPFGYGVRACLGKRIAELEMHLALSRVIR MFELRWDPKGEDIKSIARIVLSPSKPVNLQFLERKTHQE